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- PDB-4r8i: High Resolution Structure of a Mirror-Image RNA Oligonucleotide A... -

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Basic information

Entry
Database: PDB / ID: 4r8i
TitleHigh Resolution Structure of a Mirror-Image RNA Oligonucleotide Aptamer in Complex with the Chemokine CCL2
Components
  • C-C motif chemokine 2
  • Mirror-Image RNA Oligonucleotide Aptamer NOXE36
KeywordsCytokine/RNA / Aptamer Spiegelmer L-oligonucleotide / Cytokine-RNA complex
Function / homology
Function and homology information


helper T cell extravasation / chemokine (C-C motif) ligand 2 signaling pathway / CCR2 chemokine receptor binding / negative regulation of natural killer cell chemotaxis / astrocyte cell migration / CCR chemokine receptor binding / positive regulation of apoptotic cell clearance / negative regulation of glial cell apoptotic process / ATF4 activates genes in response to endoplasmic reticulum stress / positive regulation of glutamate receptor signaling pathway ...helper T cell extravasation / chemokine (C-C motif) ligand 2 signaling pathway / CCR2 chemokine receptor binding / negative regulation of natural killer cell chemotaxis / astrocyte cell migration / CCR chemokine receptor binding / positive regulation of apoptotic cell clearance / negative regulation of glial cell apoptotic process / ATF4 activates genes in response to endoplasmic reticulum stress / positive regulation of glutamate receptor signaling pathway / NFE2L2 regulating inflammation associated genes / chemokine-mediated signaling pathway / eosinophil chemotaxis / cellular homeostasis / negative regulation of vascular endothelial cell proliferation / chemokine activity / Chemokine receptors bind chemokines / negative regulation of G1/S transition of mitotic cell cycle / positive regulation of macrophage chemotaxis / positive regulation of calcium ion import / chemoattractant activity / macrophage chemotaxis / Interleukin-10 signaling / monocyte chemotaxis / humoral immune response / cellular response to interleukin-1 / positive regulation of endothelial cell apoptotic process / G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger / cell surface receptor signaling pathway via JAK-STAT / positive regulation of synaptic transmission, glutamatergic / cellular response to fibroblast growth factor stimulus / cytoskeleton organization / sensory perception of pain / viral genome replication / animal organ morphogenesis / response to bacterium / positive regulation of T cell activation / cellular response to type II interferon / cytokine-mediated signaling pathway / chemotaxis / antimicrobial humoral immune response mediated by antimicrobial peptide / cellular response to tumor necrosis factor / regulation of cell shape / cellular response to lipopolysaccharide / angiogenesis / Interleukin-4 and Interleukin-13 signaling / negative regulation of neuron apoptotic process / cell surface receptor signaling pathway / protein phosphorylation / protein kinase activity / cell adhesion / positive regulation of cell migration / G protein-coupled receptor signaling pathway / inflammatory response / signaling receptor binding / positive regulation of gene expression / signal transduction / extracellular space / extracellular region
Similarity search - Function
CC chemokine, conserved site / Small cytokines (intercrine/chemokine) C-C subfamily signature. / Chemokine beta/gamma/delta / Intercrine alpha family (small cytokine C-X-C) (chemokine CXC). / Chemokine interleukin-8-like domain / Chemokine interleukin-8-like superfamily / Small cytokines (intecrine/chemokine), interleukin-8 like / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #40 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
: / STRONTIUM ION / RNA / RNA (> 10) / C-C motif chemokine 2
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.05 Å
AuthorsOberthuer, D. / Achenbach, J. / Gabdulkhakov, A. / Falke, S. / Buchner, K. / Maasch, C. / Rehders, D. / Klussmann, S. / Betzel, C.
CitationJournal: Nat Commun / Year: 2015
Title: Crystal structure of a mirror-image L-RNA aptamer (Spiegelmer) in complex with the natural L-protein target CCL2.
Authors: Oberthur, D. / Achenbach, J. / Gabdulkhakov, A. / Buchner, K. / Maasch, C. / Falke, S. / Rehders, D. / Klussmann, S. / Betzel, C.
History
DepositionSep 2, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 29, 2015Provider: repository / Type: Initial release
Revision 1.1May 6, 2015Group: Database references
Revision 1.2Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: C-C motif chemokine 2
B: Mirror-Image RNA Oligonucleotide Aptamer NOXE36
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,0479
Polymers21,7412
Non-polymers3067
Water2,000111
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1980 Å2
ΔGint-25 kcal/mol
Surface area9730 Å2
Unit cell
Length a, b, c (Å)108.912, 108.912, 34.812
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-103-

HOH

DetailsThe biological assembly is a dimer generated from the complex in the asymmetric unit by the following symmetry operation: y,x,-z-2

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Components

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Protein / RNA chain , 2 types, 2 molecules AB

#1: Protein C-C motif chemokine 2 / HC11 / Monocyte chemoattractant protein 1 / Monocyte chemotactic and activating factor / MCAF / ...HC11 / Monocyte chemoattractant protein 1 / Monocyte chemotactic and activating factor / MCAF / Monocyte chemotactic protein 1 / MCP-1 / Monocyte secretory protein JE / Small-inducible cytokine A2


Mass: 8830.239 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CCL2, MCP1, SCYA2 / Production host: Escherichia coli (E. coli) / References: UniProt: P13500
#2: RNA chain Mirror-Image RNA Oligonucleotide Aptamer NOXE36


Mass: 12910.646 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: The NOX-E36 L-oligonucleotides with the sequence 5'-GCACGUCCCUCACCGGUGCAAGUGAAGCCGUGGCUCUGCG-3' were synthesized using standard phosphoramidite chemistry at NOXXON Pharma AG (Berlin, Germany)
Source: (synth.) synthetic construct (others)

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Non-polymers , 4 types, 118 molecules

#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-SR / STRONTIUM ION


Mass: 87.620 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Sr
#5: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: K
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 111 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.38 Å3/Da / Density % sol: 48.38 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: After thorough optimization of crystallization conditions needle shaped crystals (approx. 300x50x50um) could be obtained by mixing 1uL of the NOX-E36-CCL2 complex (in 20 mM HEPES pH 7.4, 100 ...Details: After thorough optimization of crystallization conditions needle shaped crystals (approx. 300x50x50um) could be obtained by mixing 1uL of the NOX-E36-CCL2 complex (in 20 mM HEPES pH 7.4, 100 mM NaCl, 5 mM KCl, 1 mM MgCl2, 1 mM CaCl2) with 1uL of a solution containing 40 mM Na cacodylate pH 5.5, 12 mM spermine tetrahydrochloride, 40 mM LiCl, 80 mM SrCl2 and 20 mM MgCl2 and subsequent vapor-diffusion equilibration against 1 mL of reservoir (35% (v/v) MPD, 5 mM KCl, 1 mM MgCl2 and 1 mM CaCl2). Crystals used for data collection grew within three weeks at 277K. VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.978 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 14, 2013
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.05→100 Å / Num. obs: 24915 / % possible obs: 99.2 % / Observed criterion σ(F): -3 / Observed criterion σ(I): 0 / Biso Wilson estimate: 36.4 Å2

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Processing

Software
NameVersionClassification
MxCuBEdata collection
PHENIXmodel building
REFMAC5.8.0073refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.05→77.01 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.925 / SU B: 4.071 / SU ML: 0.113 / Cross valid method: THROUGHOUT / ESU R: 0.215 / ESU R Free: 0.189 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.24971 1348 10.1 %RANDOM
Rwork0.20003 ---
obs0.20504 12058 97.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.728 Å2
Baniso -1Baniso -2Baniso -3
1-0.21 Å2-0 Å2-0 Å2
2--0.21 Å20 Å2
3----0.41 Å2
Refinement stepCycle: LAST / Resolution: 2.05→77.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms544 853 7 111 1515
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0231506
X-RAY DIFFRACTIONr_angle_refined_deg1.6092.6172149
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.36567
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.66224.16724
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.37815107
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.514154
X-RAY DIFFRACTIONr_chiral_restr0.0740.2279
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021813
X-RAY DIFFRACTIONr_mcbond_it2.0984.206271
X-RAY DIFFRACTIONr_mcangle_it3.6336.269337
X-RAY DIFFRACTIONr_scbond_it1.5363.0221235
X-RAY DIFFRACTIONr_long_range_B_refined5.02428.6192737
LS refinement shellResolution: 2.049→2.103 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.302 87 -
Rwork0.231 771 -
obs--88.91 %

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